5EPD

Crystal structure of Glycerol Trinitrate Reductase XdpB from Agrobacterium sp. R89-1 (Apo form)

Summary for 5EPD

• Entry DOI: 10.2210/pdb5epd/pdb
• Related: 4JIC
• Descriptor: Glycerol trinitrate reductase (2 entities in total)
• Functional Keywords: old yellow enzyme family tim barrel fold gtn reductase xenobiotic degradation, oxidorecctase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 1
• Total formula weight: 41141.84

Authors

Kolenko, P.,Zahradnik, J.,Zuskova, I.,Cerny, J.,Palyzova, A.,Kyslikova, E.,Schneider, B. (deposition date: 2015-11-11, release date: 2016-11-23, Last modification date: 2024-05-08)

Primary citation

Zahradnik, J.,Kolenko, P.,Palyzova, A.,Cerny, J.,Kolarova, L.,Kyslikova, E.,Maresova, H.,Grulich, M.,Nunvar, J.,Sulc, M.,Kyslik, P.,Schneider, B.
The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form.
PLoS ONE, 13:e0195299-e0195299, 2018

PubMed Abstract: Old Yellow Enzymes (OYEs) are NAD(P)H dehydrogenases of not fully resolved physiological roles that are widespread among bacteria, plants, and fungi and have a great potential for biotechnological applications. We determined the apo form crystal structure of a member of the OYE class, glycerol trinitrate reductase XdpB, from Agrobacterium bohemicum R89-1 at 2.1 Å resolution. In agreement with the structures of the related bacterial OYEs, the structure revealed the TIM barrel fold with an N-terminal β-hairpin lid, but surprisingly, the structure did not contain its cofactor FMN. Its putative binding site was occupied by a pentapeptide TTSDN from the C-terminus of a symmetry related molecule. Biochemical experiments confirmed a specific concentration-dependent oligomerization and a low FMN content. The blocking of the FMN binding site can exist in vivo and regulates enzyme activity. Our bioinformatic analysis indicated that a similar self-inhibition could be expected in more OYEs which we designated as subgroup OYE C1. This subgroup is widespread among G-bacteria and can be recognized by the conserved sequence GxxDYP in proximity of the C termini. In proteobacteria, the C1 subgroup OYEs are typically coded in one operon with short-chain dehydrogenase. This operon is controlled by the tetR-like transcriptional regulator. OYEs coded in these operons are unlikely to be involved in the oxidative stress response as the other known members of the OYE family because no upregulation of XdpB was observed after exposing A. bohemicum R89-1 to oxidative stress.

PubMed: 29630677
DOI: 10.1371/journal.pone.0195299

Experimental method

X-RAY DIFFRACTION (2.1 Å)